The machines are "GOD"
People live within the Matrix, a world that the was CREATED by machines. Although they are programs they supply water, air, food, light, weather for everyone in that world. When people pray, who is directly listening?? machines. Theyre plugged into a machine, Im sure they could read their thoughts. Im sure the matrix started out small, perhaps the first two people plugged in can be represented as Adam and Eve, even if the system did crash and had to be reloaded. Maybe a version being realoded can be represented by the GREAT FLOOD. Of course the machines can write a weather program to create and input an impossible excess amout of H2O into the atmosphere. hmmm. Perhaps "was a man born within the matrix who had the power to change it as he saw fit... blabla" Could this be represented by Jesus? Can "the one" be the next son of "God" or the machines, created for a particular purpose? Maybe the ONE was intentionally created by the machines?
Im getting all biblical, although Im no religious expert, because Ive seen a review where it says in Revolutions, Neo is "searching for God" or something to that effect, so Im thinking this might have a religious twist.